Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations.

ABSTRACT: Next-generation sequencing (NGS) technologies enable new insights into the diversity of virus populations within their hosts. Diversity estimation is currently restricted to single-nucleotide variants or to local fragments of no more than a few hundred nucleotides defined by the length of sequence reads. To study complex heterogeneous virus populations comprehensively, novel methods are required that allow for complete reconstruction of the individual viral haplotypes. Here, we show that assembly of whole viral genomes of ∼8600 nucleotides length is feasible from mixtures of heterogeneous HIV-1 strains derived from defined combinations of cloned virus strains and from clinical samples of an HIV-1 superinfected individual. Haplotype reconstruction was achieved using optimized experimental p

SUBMITTER: Giallonardo FD 

PROVIDER: S-EPMC4132706 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature